Philip Pullman answers the door. Pale skin and white shirt, he looks like a puff of smoke in the dark of the hallway. Behind him stands a dog on wheels and, further back, two real pugs, bleating, just a little, at this morning's commotion. The photographer is already in the living room. "I have that sort of face that doesn't come out well in photographs," Pullman tells him as the camera snaps away. In fact, he has precisely the type of face that bears being photographed; in pictures, it is somehow easier to focus on him, better to inspect the kindly set of his features and the grey-green of his eyes. In the flesh, you rather suspect that he has developed a subtle way of not being seen.

Pullman, 63, is the former teacher who found fame as the bestselling author of His Dark Materials, a trilogy of fantasy novels that was marketed at young adults, but found equal popularity among older readers. The series, described as an inversion of Milton's Paradise Lost, explored the effects of institutionalised religion and prompted criticism from many Christian groups. This spring, as if to bait the bear further, he has published a new book, The Good Man Jesus and the Scoundrel Christ, part of the Canongate Myths series, and a rumination on the life of Jesus, casting him not as one man, but two brothers, the prophet Jesus and his manipulative twin, Christ.

Pullman was inspired, he says, calmer now that the photographer and his camera have departed, by a conversation with the Archbishop of Canterbury, on stage at the National Theatre. "He asked me why I hadn't dealt with Jesus in His Dark Materials. And I said, 'Well you're right, I haven't, so I'd better do a book sometime.'" A while later, he had an idea (best not to call it a vision) of "the two brothers locked in argument in the desert. It was the temptation of Jesus, not by sin, but by Christ. There's the original prophet with the pure vision blazing in his mind and he's being tempted by the organisation man, who's saying, 'Well, we can set something up here, get something permanent going in the world, but we have to make a few compromises.'"

But in truth he had for some while been thinking about Jesus. "Reading around the subject," he says. "I love late antiquity because it's a time of immense competition among religions. The old gods, the Greek and Roman gods, were gradually being replaced by rather fearsome or demanding new gods, such as the one that the Christians were bringing from the region we call Palestine. At the same time, Greek thought had combined with religious feelings from a little further east and produced something then known as gnosticism . . . "

It is at moments like this, that one sees the remnants of Pullman the teacher. "It's the idea that this world is a false creation of an evil demiurge," he continues, voice calm and dry, "and not the real place created by the real God, and that all of us have inside us a sort of spark of divinity that was stolen from the real God and that explains what our task is — we have to escape and get back to the real source." He smiles faintly. "Now that's a hell of a good story because it accounts for so many things: it accounts for why there's evil and suffering and sickness and so on; it accounts for why those who think deeply don't feel at home in the world; and it gives us something to do. It's one of the best stories of all time. But it's not true." He adds a polite qualification: "I don't think."

When did he decide it wasn't true? "Well I went through a very gnostic phase in my 20s," he recalls. "I read a lot of stuff about it and tried to feel the sort of angst appropriate to someone who's a prisoner of a material world. But I don't do angst very well. As the man who wanted to be a philosopher said to Dr Johnson, 'Cheerfulness keeps breaking through.' Heh-HA!" He has a linty sort of laugh, not hearty or loud, but something quickly brushed off.

"And so I came to realise that this world was actually rather a good place, which is full of things that make you laugh and things that make you happy and things that make you feel good physically, and so I gradually abandoned the idea of the evil demiurges who had created this ghastly world, and realised actually that this is our home, it's where we belong, and there ain't no elsewhere." He pauses. "So that's where I am now, spiritually speaking. Which I never do, because I don't like that word." What word would he use? "Um . . ." he ponders. "Philosophically speaking. Intellectually speaking. Emotionally speaking."

By the kitchen door a pug whimpers. "He wants to go and lie on his bed," Pullman says, striding across the living room, littered with Snoopy toys and board games, the paraphernalia of grandparenthood (married for 40 years to Judith Speller, he has two sons and three grandchildren). "All right old boy," he soothes the dog, opening the door. "You have to be very gentle with them. It's not his fault he's old and silly. He's not stupid, he's innocent. Innocent of stupidity."

A great deal of Pullman's work seems to deal with the notion of duality. He has compared the plot of His Dark Materials to binary fission, the fundamental theme being "two things that were joined together, and split apart, and becoming two," he says now. "And maybe this new story . . . again it's a sort of binary thing, isn't it?"

The idea of twin brothers sprung from Paul's Epistles. "Paul refers to Christ rather than Jesus; the Gospels call him Jesus rather than Christ," Pullman explains. "And I thought that was significant. Because the Gospels want to tell us about his life, and Paul wasn't interested in his life, he was interested in what its meaning was after he was dead, the meaning of the resurrection, the meaning of this figure having come from God, being part of God, being God himself, really. Christ says at the end of the book, 'However it ends, this story, it will be a tragedy.' Because Jesus's vision could never come about, and the vision that will come about is not his. And that's how it happened."

He read a great deal around the subject before he began: the four Gospels and Paul's Epistles, in three different versions of the Bible. "I'd like to have read them in Greek, but I have no Greek and it would take too long to have learned Greek for this purpose," he says. He read the Pope's book on Jesus, AN Wilson's book on Jesus, and the work of Geza Vermes, the foremost Jesus scholar. He also read Strauss's Life of Jesus, as translated by George Eliot. "You could see what a stir that kind of thinking must have caused to devout Victorians," he says. He decided not to read any more commentators after that. "Because the thing about reading commentators or critics is that if you're in the middle of creating something and you read a very persuasive commentator, it can have a big impression on you and lead you off down an unhelpful path."

The Good Man Jesus and the Scoundrel Christ was recently reviewed in the Guardian by the Archbishop of Canterbury, Rowan Williams, a great supporter of Pullman. "I think he was generous," Pullman says. "Much more generous than might have been expected, but he is a good and kindly man. And predictably, but correctly, in effect he said, 'This wasn't as good as the Bible.'" Several critics have made a similar observation. "I know," he says, a little tetchy. "But I wasn't trying to write an alternative Gospel. What I was trying to do was tell the story of Jesus in a different kind of way. And make a fable out of it." He hopes in fact that his book will lead people back to the Bible itself. "Because then they will see how many contradictions and inconsistencies there are between the gospels," he explains, "instead of this single monolithic story."

We have, he adds, only "a vague impression" of the Bible. "If we have a Christian upbringing, we're told that Jesus was born at Christmas and all the shepherds came, and the wise men, and the little donkey, and there was a star and so on. And then a couple of months go by, and he's betrayed and flogged and crucified and then he rose on the third day and everybody had Easter eggs and there were daffodils around and all that sort of thing. And the rest of the time he went around telling stories and curing people. So that's all we know about him. And we think that the New Testament says that. Well actually, Mark says this and Matthew says that, and Luke says something else and John says something quite different. And we don't know this, because we don't actually read the damned thing."

When does he suppose people stopped reading the Bible? Or did they ever truly read it? "Well . . ." he thinks. "Yes they did. And the history of the reading of the Bible is a book I'd like to read. Because Tyndale and the early translators got into terrible trouble and suffered enormously, because the church disapproved of the Bible in the vernacular; they wanted to keep the story for themselves and allow little bits out very parsimoniously. Eventually it was translated, of course, but the church didn't have very much to fear because most people didn't read, don't read very deeply. They will read the bits they like and ignore the bits they don't understand or don't like."

Pullman recalls reading the Bible in a similar way, growing up, under the influence of his clergyman grandfather. He remembers him as "a wonderful storyteller . . . full of anecdotes, and stories from the Bible and stories about saints and good people he had known. So I remember my childhood being full of stories, both in and out of church. He was also a prison chaplain, at Norwich prison, at a time when they still hanged people. And it was his job to spend the last hour with the condemned man. It was something that affected him deeply and painfully."

But it was not so much his grand- father's sermons, he insists, that affected his own storytelling so much as the years he spent as a teacher. "Telling stories aloud and making up stories. You learn such a lot when you tell great stories like the Iliad or the Odyssey, over and over again. You learn what a good story shape is, you learn how to time it — I used to like getting to a good bit just when I knew the bell was about to go. It gave me great pleasure when they wanted to stay in rather than go out and play." Pullman talks quite tenderly about his past.

"And you learn what you can do and what you can't do," he adds. "I can't do funny stories. Can't do them at all. I can do them on the page, but I can't deliver them. There's something I haven't got. And I've tried, but I haven't got it. But I can do tension and suspense and action, and I can paint a scene so that it comes clearly before the listeners."

It reminds me of a conversation that takes place in The Good Man Jesus, where Christ visits a prostitute and afterwards discusses his brother, depicting him as a man of passion, while all he can do is describe what happens. "Ah," smiles Pullman, "his postcoital self-analysis." Does he see himself as the passionate being or the describer? "Oh I'm the describer," he says firmly, resolutely. "That's what I do." Has he always felt that way? "Oh yeah," he says. "I've always noticed things, watched how they happen and how people deal with them. And then gone over them in my mind, made them better, shaped them, cut out the extraneous stuff. There's part of me that looks at everything, always, that's always on duty. Maybe that's true of everyone," he says brusquely, "and they just call it daydreaming."

But is there anything in his life that carries him away? Any passion or obsession that forces him to put aside his describing self? He thinks for a long, silent while. "Well I get very exercised about politics and civil rights," he says eventually. "But, as I've learned, if you just say the first thing that comes into your head you get carried away by a wave of passion, you tend to spout nonsense and gibberish, so it's much better to be dispassionate about it ahead of time. It's not the fury you remember afterwards; it's cool words that are said by somebody who has thought about them." He admires especially Clive Stafford-Smith as a contemporary orator. "But do we have people of that stature in British politics?" he asks, pre-empting my question. "No, not one."

He will be voting for Evan Harris, his local Liberal Democrat MP. He has been voting for him since 1997, "when I wanted a Labour government after 18 years of the wretched Tories, but the stupidity of our voting system is that if I wanted a Labour government I had to vote against the Labour candidate in my constituency." He bridles. What does he think of the Tories' latest incarnation? "Oh they're very smooth and personable," he smiles. "But I don't trust them as far as I could throw them."

The other subject of his vitriol is the Catholic church. "It's been caught with its trousers down, in many different ways, hasn't it?" he says of the recent abuse scandals. "They didn't expect this sort of thing to happen, this sort of thing to come out; they didn't expect to have to account for themselves in the way that they've had to. But this is what happens, always, when you have an organisation whose authority derives from something that may not be questioned.

"Now," he continues, "when you get that sort of authority, in any set-up, the potential for corruption is wide open. And when it comes to looking after children or people who are incapable or helpless, well human beings are tempted. And of course part of the reason it happens is priestly celibacy. They'll deny it and say it's nothing to do with that, but of course it is, of course it is. That's not to say that married men are free from temptation or never given way to it, because of course they have, but the level of frustration and unhappiness and unfulfillment that must build up in a man who's denied one of the most important aspects of his humanity, it'll get bad."

I ask him if he thinks the scandal will change the Catholic church. "I hope so," he says quickly, and then draws back. "Well why do I hope so? In one way, I hope the wretched organisation will vanish entirely. So I'm looking on with a degree of dispassionate interest." He does not, at this moment, seem so dispassionate.

I wonder if he now feels a responsibility to write about religion. "No," he says firmly. "I write when my imagination prompts me. I don't write out of will or out of conscience or anything else. When my imagination is next engaged about religion I shall write about it again." But it is impossible not to wonder if he rather enjoys the reputation as a well- regarded critic of the church. "Well I don't know what my reputation is," he answers flatly. "A humourless, tedious atheist probably."

• The Good Man Jesus and the Scoundrel Christ by Philip Pullman is available now in hardcover (£14.99), ebook (£12.99), audiobook (16.99)and App (£9.99) from Canongate.